[gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 89

[niki24 at tezu.ernet.in]

> Message: 1
> Date: Thu, 24 May 2018 17:31:00 +0530
> From: niki24 at tezu.ernet.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] AMP_simulation
> Message-ID:
> 	<6be73c5ff3ffc470d178638a18b6e33f.squirrel at webmail.tezu.ernet.in>
> Content-Type: text/plain;charset=utf-8
>
> Hello,
>
> I have tried doing the Molecular dynamics simulation of AMP using the
> Gromos54a7 forcefield.
>
> ITP parameters for the AMP molecule has been generated using the ATB
> builder. Minimization of the molecule goes on well however while carrying
> out the Nvt theres a segmantation fault resulting in step files.
>
> Moreover LINCS warning are shown with bonds that rotated more than 30
> degrees. ihave tried changing lincs parameter and also increasing the step
> size, but still simulation crashes.
>
> Is it suggestible to generate topology for the AMP molecule from the
> available topological parameters of ATP in GROMACS. Or are their any
> source of getting the correct itp paremeters for "AMP".
>
> Thanks
> Nikita Bora
>
>

>
> Message: 2
> Date: Thu, 24 May 2018 18:38:53 +0530
> From: Soham Sarkar <soham9038 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
> 	<CA+fBedf9KeoopU-wLqhVEGaO0DeNbo+HCb9d4Jz6-6tHQEY9yw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Try with 1ps time step
>
> On Thu, 24 May 2018, 6:33 pm , <niki24 at tezu.ernet.in> wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>> Thanks
>> Nikita Bora
>>
>>
>>
>
> Message: 3
> Date: Thu, 24 May 2018 18:43:01 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
> 	<CAAtfiTsdz0TDtoHfCArSVyFmKTcGG3tUeQ07+jtm7vKuwvYomQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi
>
> On Thu, May 24, 2018 at 5:31 PM, <niki24 at tezu.ernet.in> wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>
> Segmentation fault normally occurs for large system with small memory.
> You
> can write xtc which is a compresssed trajectory file.
> Adding time steps to write the file.
>
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>
> Lincs warning, as for here without knowing exactly about the system, i
> think the error is due to improper minimization.
> Minimize properly ir go for double precision method.
>
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>
> Yeah, not an issue I guess.
>
>>
>> Thanks
>> Nikita Bora
>>
>
> Thanks back
>
-
> *Regards,*
> *Rahul *
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 24 May 2018 18:43:01 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] AMP_simulation
> Message-ID:
> 	<CAAtfiTsdz0TDtoHfCArSVyFmKTcGG3tUeQ07+jtm7vKuwvYomQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi
>
> On Thu, May 24, 2018 at 5:31 PM, <niki24 at tezu.ernet.in> wrote:
>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>
> Segmentation fault normally occurs for large system with small memory.
> You
> can write xtc which is a compresssed trajectory file.
> Adding time steps to write the file.
>
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>
> Lincs warning, as for here without knowing exactly about the system, i
> think the error is due to improper minimization.
> Minimize properly ir go for double precision method.
>
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>
> Yeah, not an issue I guess.
>
>>
>> Thanks
>> Nikita Bora
>>
>
> Thanks back
> --
> *Regards,*
> *Rahul *
>
>
>
Hello,
Thanks for your suggestions, i have attached herewith the coordinate file
of amp and also the itp file.

If i could get any suggestion whether the itp file generated is correct
for my molecule.

Thanks
Nikita Bora


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